8C5N

Sub-atomic resolution structure of the chitin-binding protein D (CbpD) from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	150 mM NaCl, 15 mM Tris-HCl pH 7.5, 0.2 M ammonium chloride, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.6	α = 90
b = 54.56	β = 99.246
c = 47.98	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)	2020-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.65255	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	0.75	47.4	97	0.055	0.056	0.012	0.999	20.9	19.9		198464			6.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.75	0.76	76		0.3	0.6	8.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	0.75	47.357	196572	9879	96	0.154	0.1537	0.1634	10.591

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.031		0.007	0.026		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.172
r_dihedral_angle_6_deg	18.188
r_dihedral_angle_3_deg	14.692
r_dihedral_angle_1_deg	7.023
r_rigid_bond_restr	3.673
r_lrange_it	2.464
r_lrange_other	2.283
r_angle_refined_deg	2.072
r_scangle_it	1.923
r_scangle_other	1.899
r_scbond_other	1.66
r_scbond_it	1.574
r_mcangle_it	1.562
r_mcangle_other	1.277
r_mcbond_it	1.124
r_mcbond_other	0.96
r_angle_other_deg	0.689
r_xyhbond_nbd_refined	0.346
r_nbd_refined	0.27
r_nbtor_refined	0.219
r_symmetry_nbd_other	0.212
r_symmetry_nbd_refined	0.205
r_nbd_other	0.16
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.106
r_chiral_restr	0.105
r_gen_planes_other	0.019
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1412
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
SHELXL	refinement
PHENIX	refinement
Coot	model building